Metroid: Origins
by Flareod
Summary: The discovery of two ancient and unidentifiable ships in the UPC357GG1 system leads the Federation on a hunt to find their origin before the Space Pirates can use these new ships’ power to take over the galaxy.
1. The Terran Ship Ionian

**Metroid: Origins**

**Summary: **

The discovery of two ancient and unidentifiable ships in the UPC-357GG1 system leads the Federation on a hunt to find their origin before the Space Pirates can use these new ships' power to take over the galaxy.

**Fic Rating: **T/PG-13 for Violence and Language

**Chapter Rating:** K+

**Warnings: **Spoilers for all released Metroid games.

**Disclaimer:** I do not own Metroid, any affiliated characters, stories, places etc. This story is a non-profit venture and was not written with the intention of making money.

**A/N:** This is my first story in something like 2 years - and my first Metroid fic - so I'm probably a bit rusty. Con-crit and any hints or suggestions are defiantly welcome. _On this chapter_: It's really a prologue, but for the sake of not going insane when it comes to chapter numbers on the drop-down menu I'm just leaving it as Chapter 1. None of these characters are major or recurring.

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**Chapter 1:** Last Flight of the Ionian (Prologue)

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The Terran ship Ionian exited hyperspace just outside UPC-357GG1, a small unexplored, planetary system on the outskirts Galactic Federation territory. For those in the bridge of the star ship it was a sight to behold as they passed by the six beautiful gas giants, each surrounded by their own mini-system of moons. However, the Ionian was on a search and rescue mission, so admiration of the aesthetic beauty of the planets would have to wait.

"Have we got a clear lock on the distress signal?" asked Captain William Lockheart to his communications officer.  
"Affirmative sir. It's near the third planet from the sun, the signal seems to be coming from the smallest moon," she replied bringing up a hologram of the planet - moon highlighted - for the crew to see. Lockheart nodded and proceeded to open up a communications link with the Galactic Federation outpost that had alerted him of the signal.  
"This is the Earth Ship Ionian reporting to Galactic Federation outpost on Kerkon V. We have identified the location of the mysterious distress signal," reported the Captain.  
"Thank you Captain Lockheart. Can you send us a constant visual stream?" reported the squid-like entity on the other end of the line. The Captain nodded in agreement and instructed the crew to activate the sub-light engines.

Lockheart sat back in his chair and contemplated what they might find. The distress signal was broadcast in most Federation languages _and_ several unknown dialects. It was obvious that a highly advanced race was sending this message, quite possibly the chozo; although he would not admit this to his crew just yet. If so, the more urgent question was: What could make a chozo ship send out a distress signal?

"Captain we have a visual of the moon," informed someone from the deck, breaking William's thought. "But the scanners are picking up more than one ship on the surface."  
Projected in the centre of the bridge was a hologram of two separate, and distinctly different ships, both of which were suffering severe hull damage. Results of the initial scans were presented to Lockheart on a hand-held computer device. It seemed that only the passengers on one ship managed to survive.

He re-opened the transmission with the Kerkon V outpost and sent the data to the overseer on the other end. Hopefully the federation databanks would be able to determine the origin of the ships.  
"William, we have discovered something very interesting…" he paused. "It would seem that ships of this design are not on any records."  
"Not even out-dated records?" asked Lockheart.  
"I've run a full search of the database and cross-compared with all available informatio…" but before the overseer could respond, the transmission ceased. Lockheart looked around to see if any of his crew had made the move.

"What's going on?" he called, rage filling his voice.  
"Sir it would seem that our transmission is being blocked," answered the communications officer, frantically typing at her post. She froze for a moment, a look of horror spreading across her face. "Sir we have a Code Black. I repeat; Code Black. A Space Pirate vessel has exited hyperspace just outside the system." The hologram changed to a map of the system, showing the location of both ships. Readings showed that at the current rate there would be an encounter within five minutes. Suddenly another blip appeared on the hologram; another Space Pirate ship had emerged. Everyone turned to look at Lockheart.

"I think it would be safe to assume that we would have an exceptionally low chance of success if we stay and fight. I believe our best course of action is to try and get out of the system, send a message to the Kerkon V outpost make a jump to hyperspace as quickly as possible," he instructed. But as he concluded, two more ships appeared on the hologram. Unlike the other two, both of the newcomers were destroyer-class ships which meant they were heavily armed and very effective at eliminating threats. It was quickly becoming obvious that there wasn't much hope of escape. It was then he made his decision.

"Lieutenant," he said, addressing his second in command. "I would like all of our hyperspace capable shuttles launched, however they are not to engage the enemy. Their mission will be to carry as many passengers as possible to the nearest safe-zone and to alert the Federation to what is going on. To fly them pick our best pilots. The remaining crew will remain on-board. We will try to escape, however it does not look like we will succeed. Send out the order immediately, we have about 3 minutes until we engage the enemy."

Lockheart turned away from his crew to stare out the window at the sun of UPC-357GG1, admiring the last vista he would ever see…


	2. The Hunted

**Metroid Origins**

**Summary:**

The discovery of two ancient and unidentifiable ships in the UPC-357GG1 system leads the Federation on a hunt to find their origin before the Space Pirates can use these new ships' power to take over the galaxy.

**Fic Rating:** T/PG-13 for Violence and Language

**Chapter Rating:** T

**Disclaimer: **I do not own Metroid, any affiliated characters, stories, places et. This story is a non-profit venture and was not written with the intention of making money.

**A/N:** Well to anybody who's been reading the story I apologise about the delay, but I had the last term of Grade 12 which was great – I'm now graduated – and then I was away for a while. Then there was the writers block (this is about the fourth different chapter 2 I've written). Hopefully I'll be more regular from now on.

**Chapter 2: The Hunted**

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Within a small one-man space shuttle in orbit around the planet PR-296, Kieran Joldernan reviewed data for his current mission. On the screen in front of him was intelligence from a trusted source, one who claimed to have information on his latest prey. Ever since the B.S.L. space station incident, bounty hunters such as Joldernan had been on the greatest hunt the galaxy had ever known: the hunt for Samus Aran. Despite her previous relationship with them, the Federation had placed a bounty on the "Hero of the Galaxy's" head of 300,000,000 Federation Credits on charges of "Willful Destruction of Federation Property and Equipment", "Wilful Destruction of Federation Research", "Obstruction of Justice" and the greatest surprise to all who heard it, "Wilful Geocide".

Knowing well that this would be one of his hardest missions yet, Kieran had to carefully plan out his moves. To his advantage he would have the element of surprise, the Federation Police and the fact that Samus' power suit was too conspicuous to wear in public.

But before the capture, he felt like a strong drink.

As he entered the 7th Sun, a bar in PR-292's major city, Joldernan eyed the room carefully. The metal walls and tables were all crafted to be practical, rather than aesthetically pleasing, and he felt it looked more like a jail or fortress than a place to come and relax. Admittedly, 7th Sun's clientele rarely attended the bar for relaxation purposes and were more likely to be in the midst of a shady and, more often than not, illegal business deal.

The hunter pulled up a stool in front of the bar and made a gesture for one of the barmaids to take his order. A young, attractive brunette with a name badge that read "Suzie" approached him and removed a notepad from between her cleavage.

"What do you want hun?" she asked nonchalantly, eyeing the stranger from head to toe.  
"I'll have a P3X-413 vodka," he replied. "And I've got a friend coming who'll want a Q7N-111 shot." The woman smiled and turned around to prepare the drinks. Joldernan studied the exits of the bar and made a mental note of their locations, taking into his calculations the probability of an exit out the back. He was well known among these circles, and if he was recognised by anyone who held a grudge he'd have to make a dash for it.

"Here, these are on the house," said Suzie, giving Kieran a wink and proceeding to turn her attention to another customer down the other end of the bar. He smirked, satisfied with her hospitality before downing both drinks.  
"Oh and Suzie…" he called after the barmaid. She paused briefly before returning to face the bounty hunter. "…or should I say Samus? In the name of the Galactic Federation, you're under arrest." In one, swift movement Joldernan removed a large laser-pistol from his coat and pointed it at her chest. The rest of the bar erupted in cries from frightened and annoyed patrons dashing towards the exits, scrambling over each other in hopes that Joldernan wouldn't come after them next.

Amidst the commotion she simply smiled and leaned over the bar so she was almost an inch from his face. "Oh Kieran, and here I was thinking that you'd never find me," she smirked. Joldernan was slightly taken aback by her confident attitude; he hadn't gambled on her recognising him.  
"Don't be so shocked, you don't get to be known as the second-greatest bounty hunter in the galaxy without people recognising you," she giggled. Indeed, at six feet with large tattoos covering his arms and huge black dreadlocks Kieran Joldernan was an easily recognisable character.  
"Who gave you the tip off?" she asked, almost mocking him. "Was it Grekin? Or maybe Dourishi. No… they were both here, but they wouldn't have recognised me."  
Kieran smirked, "It was Nobo," he said in a faux-friendly manner before returning to his usual stern self. "But that's beside the point. I'm taking you in and the feds want you alive, so I'd appreciate it if you came quietly."

"You didn't think it would be that easy did you?" whispered Samus into Joldernan's ear. In the blink of an eye, Samus' hand reached under the counter, to produce a laser pistol with which she fired three times into Kieran's chest. The male hunter was propelled across the room into one of the metal tables, colliding with a sickening crunch.

It was then that the other patrons of the establishment turned their attention to her, suddenly remembering the huge bounty on Samus' head. Realising this, she dashed across the room to Joldernan's limp body and grabbed the laser pistol that he had dropped, firing both it and her own at the aliens now attacking her. She managed to take down nine before a barrage of weapons, both projectile and energy, came down upon her. The huntress only managed to survive by flipping over a nearby table and diving behind it for protection. Samus dared a look back at the bar, and saw none of the barmaids she'd begun to call her friends. She could only hope that they'd made it out the back and were waiting for the commotion to die down.

Working at the 7th Sun had given Samus a brief reprieve from her life of endless fighting, but she'd learnt a lot more about another kind of conflict as "Suzie". Most of the girls who worked here were trying desperately to save enough money to go to university and study, or to be anywhere but there. Almost all of them had come from bad backgrounds and preferred not to talk about themselves, which suited Samus fine – considering she hadn't wished to discuss her own. But still, the girls were so tight that it was almost like a family, a family which Samus had betrayed. She hated bringing this on them, putting them in danger, but she didn't have a choice.

Suddenly, Samus was brought back to reality by a silence that was almost as bad as the commotion before it. Concerned, she quickly glanced over the top of the table and saw something that struck fear into her heart; a pair of Zebesians had entered the bar. Normally this wouldn't be a big deal, however she currently did not have access to her power suit. She heard them ask a terrified human where she was, and presumably he had gestured towards the table. She would have to think fast.

"Come out Aran, and we won't have to kill you," ordered one of the Zebesians. "We need the money, so we'd like it if you'd come with us alive." It was then that Samus had an idea. She slowly stood up, holding one of the guns to her temple.  
"If you let them get me I'll kill myself," she said bluntly, with a devious smirk. "And then nobody will get the 300,000,000 credits." The other creatures froze, shocked and confused by her actions. Bravely she added, "If you _don't_ kill them I'll shoot myself." The pirates looked around the room and, in their frustration, raised their clawed gun-arm to face Samus.

"I was hoping to bring you in uninjured, but you leave us no…" but the pirate was cut off as one of the many onlookers shot him in the back.  
"Sorry, but we need her alive," he said, as the others alongside him opened fire on the Space Pirate. Normal weaponry was not enough to pierce the armour, but a barrage of shots was more than enough to do significant damage. In return, the Zebesians attacked several of the warriors, taking down almost fifteen before they themselves were terminated.

At the conclusion of the brief civil war, there were a mere 13 warriors left, four of whom were wounded. Samus, not waiting for her opponents to recover shot thirteen times with her guns on the stun setting, taking down all of them. Despite the fact she had only stunned most of the people who she had shot, they would be down for more than enough time for her to escape. She quickly grabbed some more powerful weaponry from the downed fighters, along with the access card to Joldernan's space-ship before running into the back room of the bar, where she encountered the rest of the barmaids cowering in a corner.

"It's okay girls," she said. "But I'd get out of here if I were you before some more weirdos arrive." They all nodded as Samus headed towards the back emergency exit.

When she charged out the exit she felt a sharp, hot pain in her chest that spread out in a pins-and-needles sensation across her body, loosening her muscles and limbs, causing her to drop her weapons. In less than a second she was unable to hold herself upright and she collapsed on the ground. As her consciousness faded and fog clouded her vision, she saw a small squadron of Galactic Federation troops running down the alleyway towards her.

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Please remember to R+R, and Con-crit is always welcome. I also apologise for any minor formatting errors, FF.N mucks up the formatting and I'm not entirely sure how to fix it. 


	3. Corridors of Power

**Metroid Origins**

**Fic Rating:** T/PG-13 for Violence and Language

**Chapter Rating:** T

**Disclaimer: **I do not own Metroid, any affiliated characters, stories, places et. This story is a non-profit venture and was written purely for your entertainment and mine.

**A/N:** I had initially abandoned this story before being struck by the urge to write some more. In the very first draft of _Origins_ the story started here, with Samus in jail. I apologise in advance for the copious amounts of dialogue. Please note that as I live in Australia I haven't played Corruption and, as a result, this story may conflict with some information from that game. Also I can't promise that chapter 4 will come soon. Finally, I apologise for any minor formatting errors and/or spelling mistakes. FF.N has a habit of messing up the spacing, and although I do proof my stories sometimes words can slip through (especially when I write late at night).

**Chapter 3:** Corridors of Power

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Several hours later, Samus' eyes fluttered open. Her first reaction was to reach for the holster that was strapped to her waist, or more accurately; the holster that was previously strapped to her waist. Mumbling a curse under her breath, Samus realised that while unconscious she had been changed into standard Federation prison gear and was completely disarmed. After examining her own body, the hunter shifted her attention to the room she was held in, not that there was much to see. To her it looked simply like a concrete rectangle with a high roof, a toilet and a niche in the wall that contained a wafer-thin mattress and pillow. It puzzled her how she managed to get into the room without any visible doors or openings of any sort.

Samus propped herself up and attempted to stand, only succeeding in reintroducing her head to the floor. It seemed that her legs were still numb from the stunner blast. Straining her arm muscles with the effort, she managed to drag her body over to the niche where the bed was located. Climbing onto the bed proved even more strenuous, and by the time she had completed the seemingly impossible task beads of sweat had formed all over her body. _This is ridiculous!_ she thought to herself. _I haven't actually done anything wrong._ Samus spent the next couple of hours quietly brooding to herself, angry at what the Federation was making her go through.

And once she had finished with brooding, she moved onto scheming.

After an undefined amount of time, a small levitating device appeared in the cell. Samus, too wrapped up in her own thought to pay attention its entrance, didn't notice the machine's presence for at least a minute. Letting out a small yelp of surprise, Samus swung herself around so that she was sitting on the edge of the bed. She examined the odd device. It appeared to be a white sphere, no larger than the side of her fist, with a camera lens protruding from the front. There was a tiny shimmer beneath it, indicating some kind of hidden anti-gravity technology. Silently, a tiny speaker slid out of the sphere.

"Greetings Ms Aran," said a voice coming from the speaker. It sounded impossibly deep and exceedingly gravely – like a deep bass who had smoked a lot. It was definitely not human. "I thought we'd never find you – I'd almost given up hope. But there you were, on a federation planets nonetheless! How amazingly careless of you…"  
"Possibly," said Samus enigmatically. "Whom do I have the pleasure of speaking with?"  
"Forgive my manners, I forgot to introduce myself. I am Prime Minister Shi'ran Nuh'lah of the Galactic Federation, no doubt you've heard of me." Samus froze, and a number of her questions were immediately answered. Nuh'lah was of a humanoid avian race, in a similar biological class to the Chozo, and as a result had a deep, raspy and non-human voice. He was also known as a just, but ruthless leader who would not tolerate criminal activity or disobedience of federation law.

"Of course Prime Minister, forgive me for not recognising your voice," Samus said with faux politeness.  
"Before I begin, Ms Aran, I really must congratulate you on your effort on PR-296. Managing to take down Joldernan _and_ a bar of angry criminals is no easy task…" began the Prime Minister.  
"How about we cut the crap and you tell me what you want," interjected Samus. She paused, waiting for a response from Nuh'lah before continuing with her own thoughts. "My guess is that you'll try and make some sort of deal. I'm too valuable for you to kill or keep locked up, so I'm gonna guess military service in exchange for my freedom. Is that right?"  
Shi'ran remained silent for a moment. Aran assumed he was consulting with a room full of political, military and legal advisors before saying anything. After the pause, he responded, "Yes, you're assumptions are correct. In exchange for 10 years of military service, we will give you your freedom…"  
"No deal," said Samus bluntly.  
"Fine then, Ms Aran, let us say… five years," Nuh'lah remained confident, despite the setback. No doubt he had expected to bargain with the hunter and had prepared accordingly for the inevitable situation.  
"I don't think you understand Mister Prime Minister, I'm not going to barter with you. In fact, I will be the one controlling this discussion," she said, a wide grin spreading across her face.  
"Ms Aran, you have committed several criminal acts that are enough to warrant the death penalty. The likelihood of you making demands is extremely slim," said the Prime Minister.  
"Contact me when you have had a look at the information stored on the data disc that can be found inside the watch you took from me when I was placed in here," she said abruptly before turning away from the camera and lying back down. This defiant gesture would almost certainly have shocked and insulted those observing the conversation from the other end, while instilling in them a fear of what was on the data disc. Samus suspected that it would be a few hours before they contacted her, so she closed her eyes and went to sleep.

"Ms Aran," said Nuh'lah's gravely voice, disturbing the hunter's sleep. "We have reviewed the data on the disc and find it… intriguing."  
"As did I when I first discovered," she replied.  
"However this detailed outline of the Metroid Breeding Program aboard Ceres isn't useful to us," he stated, before adding patronisingly, "We know about our own programs, so I hope you weren't planning on providing us useless information in exchange for your freedom."  
"Of course _you_ won't find it interesting, but I'm sure if it was broadcast to every news provider in the Federation _they_ might," she retorted, mischievous grin returning.  
The Prime Minister simply laughed, or rather, he made a guttural sound that was his race's equivalent. "And you plan on distributing it from your jail cell?"  
"No. That job is for my ship's AI," she replied sternly, the grin remaining. "He's a very smart computer. You see, if I don't contact him every 48 hours he is instructed to broadcast these details to FNNN, FBC, JI-P, KKC, MID and various newspapers and less-known networks."  
"We can just censor them," snapped Nuh'lah, a trace of fear appearing in his voice.  
"Oh please. A story this big will get out no matter how much you want it to stay quiet," she snapped in a condescending tone. The Prime Minister went silent. Samus could only presume that he was discussing his options with the aforementioned room of advisors.

While she waited for a response, Samus couldn't help but feel a little bit cocky. Her plan had worked perfectly and it was only now that Nuh'lah was realising that she had allowed herself to be captured. She also knew that if this attempt at blackmail failed, she still had a few options open to her. After waiting for a reasonable amount of time, Samus cleared her throat in an attempt to redraw focus back to herself.

"Samus," began Nuh'lah tentitavely. "I have discussed our options with a few of my close advisors, and we have decided that we will give you your freedom in exchange for a mission worth 5,000,000 Credits and your silence on the matter of the Ceres Metroid breeding program."  
"Excellent," she replied. The free mission that she was required to perform was not entirely unexpected. In fact, she was pleased by the idea, as it confirmed that the Federation still needed her around. "I suspect that you will be releasing me immediately then."  
"I'm afraid that it will be a few hours before the paperwork and documents will be cleared. But then…"  
Samus sighed before interrupting in a tone of faux concern, "Okay then, I only hope for your sake that I am released before 18:00 Federation Standard Time, because that's when Adam is programmed to broadcast the information of the breeding program."  
Nuh'lah simply replied with, "We will do our best."

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Please remember to R+R. Concrit is more than welcome, flames are not. 


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